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A new approach to biogeographical subdivision

RUSSIAN JOURNAL OF MARINE BIOLOGY 2009年第1期35卷 79-86页

作者： Sukhanov, V. V. Ivanov, O. A. Russian Acad Sci Far E Div Zhirmunsky Inst Marine Biol Vladivostok 690041 Russia Pacific Res Fisheries Ctr Vladivostok 690950 Russia

The authors propose a new approach permitting subdivision of a water area into sectors, each including species with a similar biogeographical status. This approach relies on computer methods for construction of maps presenting the spatial distribution of continuous fields. The method is illustrated by data on the nekton from the north-western Sea of Japan. Different modifications of the method and prospects of its further development are discussed.

关键词： biogeographical zoning methods computer algorithm

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The mapping and reconstitution of a conformational discontinuous B-cell epitope of HIV-1

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JOURNAL OF MOLECULAR BIOLOGY 2003年第1期334卷 87-101页

作者： Enshell-Seijffers, D Denisov, D Groisman, B Smelyanski, L Meyuhas, R Gross, G Denisova, G Gershoni, JM Tel Aviv Univ George S Wise Fac Life Sci Dept Cell Res & Immunol Tel Aviv Israel Galilee Technol Ctr MIGAL Kiryat Shmona Israel

A method for the discovery of the structure of conformational discontinuous epitopes of monoclonal antibodies (mAbs) is described. The mAb is used to select specific phages from combinatorial phage-display peptide libraries that in turn are used as an epitope-defining database that is applied via a novel computer algorithm to analyze the crystalline structure of the original antigen. The algorithm is based on the following: (1) Most contacts between a mAb and an antigen are through side-chain atoms of the residues. (2) In the three-dimensional structure of a protein, amino acid residues remote in linear sequence can juxtapose to one another through folding. (3) Tandem amino acid residues of the selected phage-displayed peptides can represent pairs of juxtaposed amino acid residues of the antigen. (4) Contact residues of the epitope are accessible to the antigen surface. (5) The most frequent tandem pairs of amino acid residues in the selected phage-displayed peptides can reflect pairs of juxtaposed amino acid residues of the epitope. Application of the algorithm enabled prediction of epitopes. On the basis of these predictions, segments of an antigen were used to reconstitute an antigenic epitope mimetic that was recognized by its original mAb. (C) 2003 Elsevier Ltd. All rights reserved.

关键词： monoclonal antibody epitope phage display computer algorithm protein conformation

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Development and validation of a computerized South Asian Names and Group Recognition algorithm (SANGRA) for use in British health-related studies

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JOURNAL OF PUBLIC HEALTH MEDICINE 2001年第4期23卷 278-285页

作者： Nanchahal, K Mangtani, P Alston, M Silva, ID Univ London London Sch Hyg & Trop Med Dept Epidemiol & Populat Sci London WC1E 7HT England

Background Studies on ethnic variations in health have played an important role in aetiological and health services research. Most routine datasets, however, do not include information on ethnicity. South Asians, one of the largest minority ethnic groups in Britain, have distinctive names that also allow differentiation of the main sub-groups with their important differences in health-related exposures and disease risks. Methods A computerized name recognition algorithm (SANGRA) was developed incorporating directories of South Asian first names and surnames together with their religious and linguistic origin. SANGRA was validated using health-related data with self-ascribed information on ethnicity. Results SANGRA was successful in recognizing South Asian origin in reference datasets, with sensitivity of 89-96 per cent, specificity of 94-98 per cent, positive predictive value (PPV) of 80-89 per cent and negative predictive value (NPV) of 98-99 per cent. Religious origin was correctly assigned in the majority of cases: sensitivity, specificity and PPV were 94 per cent, 91 per cent and 90 per cent for Hindus;90 per cent, 99 per cent and 98 per cent for Muslims;and 76 per cent, 99 per cent and 94 per cent for Sikhs. SANGRA correctly identified 76 per cent Gujerati and 70 per cent Punjabi names, although only 62 per cent of Gujerati names were sufficiently distinct to be allocated to the Gujerati-only category and only 53 per cent Punjabi names were allocated to the Punjabi-only category. However, specificity and PPV were high for both languages (respectively 97 per cent and 93 per cent for Gujerati, and 99 per cent and 97 per cent for Punjabi). Conclusions SANGRA provides a practical and valid method of ascertaining South Asian origin by name and, to a lesser degree of accuracy, of differentiating between the main religious and linguistic subgroups living in Britain. This algorithm will be useful in health-related studies where information on self-ascribed ethnicity is

关键词： South Asian ethnicity computer algorithm

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Automated detection of the phase III slope during inert gas washout testing

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JOURNAL OF APPLIED PHYSIOLOGY 2012年第6期112卷 1073-1081页

作者： Stuart-Andrews, Christopher R. Kelly, Vanessa J. Sands, Scott A. Lewis, Angela J. Ellis, Matthew J. Thompson, Bruce R. Alfred Hosp Dept Allergy Immunol & Resp Med Serv Physiol Melbourne Vic Australia Monash Univ Dept Med Nursing & Hlth Sci Clayton Vic Australia Cooperat Res Council Asthma & Airways Glebe NSW Australia Massachusetts Gen Hosp Dept Med Pulm & Crit Care Unit Boston MA 02114 USA Harvard Univ Sch Med Boston MA USA Monash Univ Ritchie Ctr Baby Hlth Res Monash Inst Med Res Clayton Vic Australia Brigham & Womens Hosp Div Sleep Med Boston MA 02115 USA

Stuart-Andrews CR, Kelly VJ, Sands SA, Lewis AJ, Ellis MJ, Thompson BR. Automated detection of the phase III slope during inert gas washout testing. J Appl Physiol 112: 1073-1081, 2012. First published December 15, 2011;doi:10.1152/japplphysiol.00372.2011.-We describe a method to determine the phase III slope for the purpose of calculating indexes of ventilation heterogeneity, S-acin and S-cond, from the multiple breath nitrogen washout test (MBNW). Our automated method applies a recursive, segmented linear regression technique to each breath of the MBNW test and determines the best point of transition, or breakpoint, between each phase of the washout. A sample set of 50 MBNW tests (controls, asthma, and COPD) was used to establish the conditions in which the phase III slope obtained from the automated technique best matched that obtained by two manual interpreters. We then applied our technique to a test set of 30 subjects (with an even number of subjects in each of the above groups) and compared these results against the manual analysis of a third independent manual interpreter. Indexes of ventilation heterogeneity were determined using both methods and compared. The phase III slopes determined by the automatic technique best matched the manual interpreter when the phase III slope was calculated from the phase II-III transition point plus the addition of 50% of the phase II volume to the end of the expiration. Calculation of the indexes S-acin and S-cond showed no overall difference between analysis methods in either S-acin (P = 0.14) or S-cond (P = 0.59) when the set threshold was applied to our automated analysis. Our analysis method provides an alternate means for rapid quantification of the MBNW test, removing operator dependence without alteration in either S-acin or S-cond.

关键词： inert gas washout computer algorithm alveolar slope

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CHARACTERIZATION OF THE INTERACTION CONSTANTS FOR THE BINDING OF 2 UNLABELED LIGANDS TO THE SITES OF A RECEPTOR - AN EXPERIMENTAL STRATEGY

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NAUNYN-SCHMIEDEBERGS ARCHIVES OF PHARMACOLOGY 1989年第5期339卷 487-495页

作者： SWILLENS, S GOURDIN, A DELAHAUT, O 1.Institut de Recherche Interdisciplinaire Université Libre de Bruxelles Campus Erasme route de Lennik 808 B-1070 Brussels Belgium

The model describing the binding of three ligands to the sites of a receptor is theoretically studied in order to characterize the binding interaction between two unlabelled ligands. For this, the binding of a third labelled ligand, the affinity of which is dependent on the presence of the unlabelled ligands, must be measured in different conditions. This paper describes an experimental strategy leading to an accurate determination of the equilibrium parameters of the model. This strategy, which assumes that the model is compatible with the data, rests on the determination of the optimal experimental conditions, i.e. the choice of the ligand concentrations which minimize the error of the parameter estimates. For this purpose, a computer program which runs on a microcomputer under the MS-DOS operating system has been elaborated on the basis of the D-optimization criterion. This work shows that such a computer analysis is essential to the determination of the optimal experimental design, even when very simple biochemical systems are considered.

关键词： Ligand binding computer algorithm D-optimization criterion

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AN algorithm FOR FINDING ALL FUNCTIONS EMBEDDED IN A RELATION

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INTERNATIONAL JOURNAL OF GENERAL SYSTEMS 1985年第2-3期10卷 187-195页

作者： SNELL, JL SUNY BINGHAMTON THOMAS J WATSON SCH ENGN APPL SCI & TECHNOLDEPT SYST SCIBINGHAMTONNY 13901 USA

The problem is posed: find an algorithm which for any givenn-dimensional relationR⊂ A1× A2× ⃛ × An, defined on a set familyA= { A1, A2, ⃛, Anrcub;,n= 1,2, ⃛, determines all functional dependences between disjoint subsets ofAwhich are embedded inR. A solution algorithm is presented, a theorem is proved that allows a simplification in the algorithm, and an efficient computer implementation (available through the General Systems Depository) is demonstrated.

关键词： algorithm computer algorithm relation function embedded function.

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A COMPUTATIONAL algorithm FOR THE POLYNOMIAL-APPROXIMATION METHOD OF SENSITIVITY ANALYSIS IN CHEMICAL-KINETICS

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JOURNAL OF THE CHINESE CHEMICAL SOCIETY 1985年第3期32卷 253-261页

作者： HWANG, JT Department of Chemistry National Tsing Hua University Hsinchu Taiwan 300 R.O.C. The author formerly a chemistry student of the National Taiwan University from 1966 to 1970 and presently a professor of Chemistry at the National Tsinghua University wishes to dedicate this paper to Dr. Chien.

AbstractThis paper describes the logic for a program developed by the author to implement the polynomial approximation method (PAM) of sensitivity analysis for general kinetic purposes. The relevant equations and numerical details of the algorithm are outlined, a flow chart is provided, and some programming considerations are discussed in detail. A listing of the PAM code is given in the appendix. The paper also gives a few suggestions for possible improvements and extensions of the present algorithm.

关键词： Sensitivity analysis chemical kinetics computer algorithm polynomial approximation method

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Influence of software parameters on measurements in automatized image-based analysis of fat tissue histology

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ACTA HISTOCHEMICA 2020年第4期122卷 151537-151537页

作者： Wiggenhauser, P. S. Kuhlmann, C. Blum, J. Giunta, R. E. Schenck, T. Univ Munich Dept Hand Plast & Aesthet Surg Pettenkoferstr 8a Munich 80336 Germany

The understanding of fat tissue plays an eminent role in plastic surgery as well as in metabolic research. Histopathological analysis of tissue samples provides insight in free fat graft survival and culture experiments help to better understand fat tissue derived stem cells (ASCs). To facilitate such experiments, modern image-based histology could provide an automatized approach to a large amount of data to gain not only qualitative but also quantitative data. This study was designed to critically evaluate image-based analysis of fat tissue samples in cell culture or in tissue probes and to identify critical parameters to avoid bias in further studies. In the first part of the study, ASCs were harvested and differentiated into adipocytes in cell culture. Histology was performed with the fluorescent dye BODIPY and the obtained digital images were analyzed using Image J software. In the second part of the study, digitalized histology of a previous in vivo study was subjected to automatized fat vacuole quantification using Image J. Both approaches were critically reviewed, and different software parameter settings were tested. Results showed that automatized digital image analysis allows the quantification of fat tissue probes with enough precision giving significant results. But the testing of different software parameters revealed a significant influence of parameters themselves on calculated results. Therefore, we recommend the use of image-based analysis to quantify fat tissue probes to improve the comparability of studies. But we also emphasize to calibrate software using internal controls in every single experimental approach.

关键词： Adipose tissue ASC Image based analysis computer algorithm Quantification Fat cells

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EXACT CONDITIONAL TESTS FOR CROSS-CLASSIFICATIONS - APPROXIMATION OF ATTAINED SIGNIFICANCE LEVELS

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PSYCHOMETRIKA 1979年第1期44卷 75-83页

作者： AGRESTI, A WACKERLY, D BOYETT, JM UNIV FLORIDA CTR NUCL SCIDEPT STATGAINESVILLEFL 32611

A procedure is proposed for approximating attained significance levels of exact conditional tests. The procedure utilizes a sampling from the null distribution of tables having the same marginal frequencies as the observed table. Application of the approximation through a computer subroutine yields precise approximations for practically any table dimensions and sample size.

关键词： chi-square computer algorithm contingency tables independence Kruskal-Wallis

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T-Align, a web-based tool for comparison of multiple terminal restriction fragment length polymorphism profiles

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FEMS MICROBIOLOGY ECOLOGY 2005年第3期54卷 375-380页

作者： Smith, CJ Danilowicz, BS Clear, AK Costello, FJ Wilson, B Meijer, WG Natl Univ Ireland Univ Coll Dublin Dept Ind Microbiol Conway Inst Biomol & Biomed Res Dublin 4 Ireland Natl Univ Ireland Univ Coll Dublin Dept Zool Dublin 4 Ireland Natl Univ Ireland Univ Coll Dublin Dept Comp Sci Dublin 4 Ireland

Terminal restriction fragment length polymorphism (tRFLP) is a potentially high-throughput method for the analysis of complex microbial communities. Comparison of multiple tRFLP profiles to identify shared and unique components of microbial communities however, is done manually, which is both time consuming and error prone. This paper describes a freely accessible web-based program, T-Align (llttp://***/similar to talign/), which addresses this problem. Initially replicate profiles are compared and used to generate a single consensus profile containing only terminal restriction fragments that occur in all replicate profiles. Subsequently consensus profiles representing different communities are compared to produce a list showing whether a terminal restriction fragment (TRF) is present in a particular sample and its relative fluorescence intensity. The use of T-Align thus allows rapid comparison of numerous tRFLP profiles. T-Align is demonstrated by alignment of tRFLP profiles generated from bacterioplankton communities collected from the Irish and Celtic Seas in November 2000. Ubiquitous TRFs and site-specific TRFs were identified using T-Alien. (c) 2005 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.

关键词： tRFLP computer algorithm community analysis

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